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The more than 400 children taken from a ranch run by a polygamous sect will stay in state custody and be subject to genetic testing to sort out family relationships that have confounded welfare authorities, a judge ruled today.

State District Judge Barbara Walther heard 21 hours of testimony over two days before ruling that the children would be kept in custody while the state continues to investigate allegations of abuse stemming from the teachings of the Fundamentalist Church of Jesus Christ of Latter Day Saints.

“This is but the beginning,” Walther said. Individual hearings will be set for the children over the next several weeks.

Walther ordered that all 416 children and parents be given genetic tests. Child welfare officials say they’ve had difficulty determining how the children and adults are related because of evasive or changing answers.

A mobile genetic lab will take samples Monday at the main shelter where children are being kept; parents will be able to submit samples Tuesday in Eldorado, closer to the ranch.

The custody case is one of the largest and most convoluted in U.S. history. The ruling capped two days of marathon testimony that descended into chaos as hundreds of lawyers for the children and parents competed to defend their clients in two large rooms linked by a video feed.

Attorneys popped up with objections in a courtroom and nearby auditorium, then queued up down the aisle to cross-examine witnesses in a mass hearing that frustrated attorneys and stretched the small-town court system.

The April 3 raid on the Yearning For Zion Ranch was prompted by a call made to a family violence shelter, purportedly by a 16-year-old girl who said her 50-year-old husband beat and raped her. That girl has never been identified.

The state of Texas argued it should be allowed to keep the children because the sect’s teaching encourages girls younger than 18 to enter spiritual marriages with older men and produce as many children as possible. Its attorneys argued that the culture put all the girls at risk and potentially turned the boys into future predators.

A witness for the parents who was presented by defense lawyers as an expert on the FLDS disputed that the girls have no say in who they marry.

“I believe the girls are given a real choice,” said W. John Walsh. “Girls have successfully said, ‘No, this is not a good match for me,’ and they remained in good standing.”

But Dr. Bruce Perry, a psychiatrist who has studied children in cults, testified that the girls will not refuse marriages because they are indoctrinated to believe disobedience will lead to their damnation.

The renegade Mormon sect’s belief system “is abusive. The culture is very authoritarian,” he said.

Perry acknowledged that many adults at the ranch are loving parents and that the boys seemed emotionally healthy. When asked whether the belief system really endangered the older boys or young children, Perry said, “I have lost sleep over that question.”

He also conceded that the children, taught from birth to believe that contact with the outside world will lead to eternal damnation, would suffer if placed in traditional foster care.

“If these children are kept in the custody of the state, there would have to be exceptional and innovative programmatic elements for these children and their families,” he said. “The traditional foster care system would be destructive for these children.”

Child welfare officials say they have been making plans to move the children from a coliseum and fairgrounds to stable homes.

Four women testified Friday, and all said they were free to make their own choices. They also said they would do whatever it took to get their children returned to them.

“We’re a peaceful people,” Lucille Nielson said. Life on their 1,700-acre gated ranch “is very peaceful. You can feel the peace when you are there. Very loving. We raise our children in a loving environment.”

But the women also acknowledged that girls get married at ages younger than the state allows.

Some of the women bowed their heads when the judge issued her order to keep the children in state custody. They left the columned courthouse stoically, ignoring questions shouted by reporters.

They’ll face more hearings, and some could be required to take steps to prove to Child Protective Services that they should be allowed to regain custody.

Texas Rangers also are investigating a Colorado woman as a “person of interest” related to calls made to a family crisis center. Police arrested Rozita Swinton, 33, on Wednesday in Colorado Springs on a misdemeanor charge of false reporting to authorities for a call she made in late February.

Authorities did not say whether a call by Swinton might be the one that triggered the raid.

But officers who searched her home found items suggesting a possible connection between Swinton and calls regarding a compound owned by FLDS in Arizona and one in Eldorado, the Texas Department of Public Safety said late Friday. The items weren’t identified.

“The information, evidence and a statement obtained from Swinton by the Texas Rangers while they were in Colorado will be forwarded to state and federal prosecutors for their review and determination as to whether Swinton will be charged with a criminal offense,” the statement said.

Swinton’s whereabouts were unknown, and it wasn’t known whether she had an attorney. A phone number for her in Colorado Springs was disconnected.

Authorities in Colorado confirmed Swinton has a history of making false reports.